Interpretive Summary: This chapter reviews what is known about the different kinds of microorganisms, especially bacteria, that live on and in cattle. Recent research shows that these microbes play in important role in animal health and nutrition. Most of the work to date has focused on cataloging the bacteria associated with the cattle rumen, and with cattle feces. The cattle rumen is important because it is the source of bacteria and enzymes that can break down cellulose. These bacteria allow the animal to survive from eating grass, but can also potentially be harnessed for a variety of industrial uses, including bioenergy. The bacteria in feces are important because they are how bacteria enter the environment, and they can contribute to the contamination of soil and water. Though great progress has been made in deeply characterizing the rumen and fecal bacterial communities of individual animals, or small groups of animals, even these microbiomes remain largely unexplored on a population level. The work performed to date, however, provides a foundation for large-scale projects looking at how the communities in these microbiomes change over time, or in response to specific diet amendments.

Technical Abstract:
Collectively, the microbes in an ecosystem consist of bacterial and fungal communities called the microbiome. The bovine microbome serves as a foundation for animal health, a reservoir for human pathogens, and, in the case of the gastrointestinal microbiomes, a potential rich source of enzymes for industrial processes and biofuel production. The first step to understanding the role of the microbiomes in cattle is to determine which microbes are present, and understand how and why they change over time. On a practical level, the initial cataloging of the microbiome members in beef cattle has focused almost exclusively on determining the diversity of bacteria from the rumen and feces – providing detailed lists of which bacteria are present in particular locations. Future work will likely expand to include information on which genes are expressed under particular circumstances. Genomic tools can also be used to investigate questions probing animal disease complexes such as mastitis and bovine respiratory disease, or to elucidate ecological relationships such as the transmission of pathogenic or antibiotic resistant bacteria from animals to humans. In this chapter we examine the work done to date in defining the structure and function of rumen and fecal micobiomes in both beef and dairy cattle. Current limitations and future directions are also included. The concept of a “core” microbiome is discussed. Though great progress has been made in deeply characterizing the rumen and fecal bacterial communities of individual animals, or small groups of animals, even these microbiomes remain largely unexplored on a population level. The work performed to date, however, provides a foundation for large-scale projects looking at how the communities in these microbiomes change over time, or in response to specific diet amendments.